The mode and tempo of genome size evolution in the subgenus Sophophora

Abstract

Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 Sophophora species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s Cmean and Moran’s I. In addition to testing the mode and rate of genome size evolution in Sophophora species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. Sophophora genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that Sophophora genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s Cmean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships.

Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

“…Assembly quality varied greatly among the 15 genomes, with an average contig N50 of 4.4 Mb, a maximum of 16.6 Mb ( D. erecta ), and a minimum of 0.6 Mb ( D. bipectinata ). For each species, assembly resulted in genome sizes that were smaller than the expected genome size ( Bosco et al 2007 ; Gregory and Johnston 2008 ; Hjelmen and Johnston 2017 ), with repetitive sequence likely accounting for the lower values than expected. We also compared assembly statistics for each of our de novo assemblies to the published assembly of each species and found that in all cases our contig N50 values were higher than those of the published assemblies but lower than the scaffold N50 values (scaffold N50 is a measure similar to contig N50, in which half of the genome is contained in linked DNA segments, or scaffolds, larger than the value given) in all but three cases ( Table 3 ).…”

Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing

“…While transposable elements are capable of substantially altering genome size and structure, the presence of indels also contributes to genome size and collinearity ( Petrov 2002 ; Gregory 2003 ; Vitte and Bennetzen 2006 ; Hjelmen and Johnston 2017 ; Kapusta et al 2017 ). Previous work in cotton suggests there exist small differences in rates between species with large and small genomes that contribute to overall genome size change ( Grover et al 2008a ).…”

Genome Size Evolution Differs BetweenDrosophilaSubgenera with Striking Differences in Male and Female Genome Size inSophophora

“…Recent work that looks at genome size evolution in a phylogenetic context, finds various patterns for change (Arnqvist et al 2015; Jeffery et al 2016; Sessegolo et al 2016; Hjelmen and Johnston 2017; Lower et al 2017). Most of these have focused on widely-diverged species.…”

“…Species in the genus Drosophila have been the subject of a wide variety of biological studies, including phylogenetics and genome size (Gregory and Johnston 2008; Van Der Linde and Houle 2008; Van Der Linde et al 2010; Hjelmen and Johnston 2017; Hjelmen et al 2019). The wealth of information available for this genus allows researchers to develop very ambitious large scale evolutionary studies with relative ease.…”

“…Although the Drosophila genus has been widely studied, much of the emphasis for genome size studies has been placed on species within Sophophora (120 records on genomesize.com, for ∼300 species in the subgenus), the subgenus which includes the very well-studied D. melanogaster (Boulesteix et al 2005; Gregory and Johnston 2008; Hjelmen and Johnston 2017; Hjelmen et al 2019). In comparison, the subgenus Drosophila has been dramatically underrepresented (52 records on genomesize.com, for the ∼1400 species in the subgenus) with few studies and low numbers of representative taxa (Schulze and Lee 1986; Bosco et al 2007; Gregory and Johnston 2008).…”